I am always on CFW and online on Sysnand. I never turn off CFW unless I'm updating the system, but then I go right back on CFW. I have modded Animal Crossing as well and haven't been banned.I use mods, cheats, and save editors on ACNH. I have done everything on CFW online except for using NSPs because that's a definite ban I was told. I use XCI with legit certificates on SX OS though. I'd say you will be fine. If you use Emunand and 90DNS you will be safe but if you do that none of the items you hack will be in your Sysnand town unless you inject the save into your nand backup and restore it every time but its a long complicated process and a pain. When you create a Emunand, it will transfer your ACNH save file to the Emunand, but after that they will be completely separate, so if you add items in Emunand, they won't show up on Sysnand, and if you progress in game on Sysnand, it won't update on Emunand unless you create a new Emunand to update it, but this would delete anything you did or hacked on the old Emunand.
Have you entered your console serial number here?
https://ismyswitchpatched.com/ what does it say?